Jmol is a free,
open-source molecule viewer for chemistry and biochemistry. It works on
multiple platforms, including Windows, Mac OS X, and Linux/Unix systems. The
software consists of three parts, all written in the Java programming
language: the Jmol applet, the Jmol application, and the Java development
toolkit, JmolViewer. The Jmol application is a standalone Java application
that runs on the desktop. JmolViewer is a set of Java “classes” that can be
integrated into other Java applications to provide molecular visualization
and analysis of chemical structure. While interesting in their own right, in
this paper we will focus on the third component of the triad, the Jmol
applet, as it is the component that can be integrated into web pages.

Jmol has many features to offer
in the fields of chemistry and biochemistry. We will highlight many of them
in this paper. Screen shots illustrating the broad variety of applications of
Jmol are shown in Figure 1. For example, Jmol supports rendering of secondary
structures of proteins and nucleic acids, it can produce animations of
chemical reactions and conformational changes, and it can help visualize
vibrations of small molecules based on quantum mechanics or molecular
mechanics calculations.

Figure 1. Some Examples of Jmol.

click on an image to open a new window using Jmol.

Recent work has added many
new capabilities (Figure 2), including the ability to select specific groups
of atoms based on connectivity and to modify bonding patterns. Jmol can now display
orbitals and other surfaces, including planes and axes that can help in the
visualization of symmetry. Most recently, Jmol can now depict a wide range of
polyhedral structures. These and many more capabilities will be highlighted
in this paper.

Figure 2. Recent additions to Jmol functionality.

click on an image to open a new window using Jmol.

Jmol supports many of the
common input and output formats, and new file reading capabilities are added
on an as-needed basis (Table 1). Compressed files are automatically
uncompressed in the browser for faster downloads.

Chemistry is often referred
to as the “molecular” science. As such, students of chemistry early on are
introduced to molecules as three-dimensional objects, and many sorts of
wooden or plastic or even paper molecular models are used in the teaching of
chemistry. To this day, many students in organic chemistry are still required
to purchase molecular model “kits” that allow the construction of a limited
set of molecular structures. These kits help students “see” the symmetries
and structural factors involved in chemical geometry and reactivity.

RasMol[1] was a key development in the history of
computer-based molecular

visualization. Roger Sayle
began developing it in 1989 as a system for

rendering 3D molecules on
raster displays. He spent several years in the

early 1990s improving
performance and porting to various systems. With the

help of the growing user
community, he continued to add functionality,

much of it related to PDB
files and biochemistry. In 1993 he released the

copyright to the public
domain and posted the source code on the internet.

One of RasMol’s most
intriguing aspects was (and still is) that it has a

scripting language which
can be used to control the visual representation

of the molecule. One could
develop lists of operations to be carried out

on the molecule in order to
showcase important aspects of the molecular

structure such as alpha helixes,
beta-pleated sheets, and hydrogen bonds.

RasMol is a stand-alone
program that requires downloading and

installation. In the mid
1990s, with increasing interest in graphical web

browsers on the internet,
there was growing demand among

chemical/biochemical
educators and researchers for a method of conveying

the three-dimensional
aspect of molecules on the web. Using the RasMol

We don't have any current plans
for an OS-X version of Macintosh or a Linux version.

Why doesn't Chime work with
Netscape 6 and 7?

Chime has been tested on a number
of platforms, including certain versions of Netscape and Internet Explorer.
The fully tested browser and operating system combinations are listed under
the Requirements link. Other combinations of operating system and browser may
work partially or not at all. Unfortunately, we don't have the resources to
test Chime on every new browser and operating system.

The Jmol Solution

This potential crisis for
chemical educators who were developing web-based content using Chime was
diffused by the timely development of Jmol.

The Java programming
language[3] was designed as a modern programming environment
for the web. Cross-platform support and safe execution of downloaded code are
fundamental to the design. Because the Jmol applet is written in Java, most
of the cross-platform porting, maintenance and installation issues associated
with the Chime plug-in do not exist. Jmol development regularly occurs on
Linux, Mac OS X and Windows systems. When a user visits a web page containing
the Jmol applet,

the program is
automatically downloaded and executed on the client’s browser without
requiring installation.

Dan Gezelter started
writing Jmol in the late 1990s with the intention of building a replacement
for XMol, an early program distributed by the MinnesotaSupercomputerCenter (now the Minnesota
Supercomputer Institute).[4] Dan, then assistant professor at the University of
Notre Dame, had started the OpenScience Project to promote open-source scientific
software. Although Dan has not been directly affiliated with Jmol for a
number of years, his early contributions as project founder were very
important.

Egon Willighagen joined the
project in 1998, contributing support for CML files and other file formats as
well as other new functionality. In 2002 he became Jmol project leader and
oversaw a number of public releases. Egon also has responsibility for
maintaining the interface between the Chemical
Development Kit software library and Jmol.

Miguel Howard joined the
project in late 2002, with the explicit goal of building Jmol into a viable
replacement for the Chime plug-in. His first major contribution was an
interpreter for the RasMol/Chime scripting language. In the spring of 2003
Miguel began designing and implementing a software-based graphics engine that
would provide cross-platform high-performance 3D functionality. He
subsequently redesigned and re-implemented the core architecture to support
efficient rendering of macromolecules with hundreds of thousands of atoms.

An extended testing period began
at the end of 2003. Through 2004 a small set of users around the world made
significant contributions to the Jmol project by testing Jmol releases and
explaining scripting behaviors of RasMol and Chime.

Tim Driscoll, because of
his extensive experience with Chime, was particularly helpful during this
process. He helped resolve a number of issues associated with macromolecules,
including definitions of protein/nucleic predefined sets and schematic
rendering of secondary structures.

Bob Hanson also got
involved during this time, developing an interactive web site providing Jmol script documentation
and examples. Feedback and contributions from Bob and other JavaScript
experts led to the development of the Jmol.js JavaScript library, which makes
introducing Jmol into web pages almost trivial.

Jmol version 10.00, a fully
functional replacement for the Chime plug-in, was released in December 2004.

As the Jmol community grew,
requests for new functionality came in. Through 2005 a number of new
scripting, rendering and file format features were introduced into the
development version of Jmol. Notable additions included support for polyhedra
representations and isosurfaces.

Nicolas (Nico) Vervelle
joined Jmol because of his interest in the Folding@home

project. He contributed the file reader for folding@home’s files and added
expressions for substructure searching using SMILES syntax. Nico then took
over responsibility for managing internationalization and localization
efforts.

Another official release, Jmol
version 10.2, was made in April 2006. It included language localizations
for Catalan, German, Spanish, Estonian, French, Dutch, and Portuguese. In the
spirit of open source development, localizations were contributed and
maintained by Jmol users from different countries.

Jmol development continues
along a variety of paths, and the Jmol community continues to grow, with
increasing involvement and interest from educators and scientists around the
world.

What follows is a
discussion of the use of Jmol in education in a variety of chemical and
biochemical contexts. The discussion highlights web sites that have utilized
Jmol, general capabilities of the current version of Jmol, and a few sneak
peeks of some of the more experimental features of Jmol not yet publicly
released. This list is by no means comprehensive. Most of these examples were
taken from the extensive list at the Jmol wiki,
which also includes examples of the use of Jmol in research.

Jmol for General and
Inorganic Chemistry

In the area of general
chemistry, Jmol has been used primarily to illustrate the various common
three-dimensional molecular shapes. Some representative sites are shown in
Table 2.

WebElements utilizes
Jmol for the display of crystal structures of the elements. The 3Dchem.com site illustrates
how easy it is to add a structure to any web page. This can be seen by taking
a peek at the source for one of
these pop-up windows. Explain
it with Molecules uses Jmol to help explain everyday questions with the
aid of 3D models. The CoolMolecules site illustrates a novel feature of Jmol –
the ability to create a 3D model of a structure on the fly – with no actual
structure file on the server. Instead, the data for all of the structures are
stored in a compressed fashion in one single
file, which is delivered to the user’s browser upon page loading. John
Gutow’s VSEPR tutorial and Mark Winter’s Introduction to
VSEPR are both excellent examples of the integration of Jmol into an
online lesson in bonding theory and its association to molecular shape and
electronic configuration.Richard
Spinney (OhioState) has developed an amazing site, “Dr.
Spinney’s World of Chemistry” that employs Jmol in a wide variety of
creative ways. Several web sites use Jmol to depict atomic and molecular
orbitals in terms of probability, using Jmol “atoms” to represent positions
around the nucleus. Finally, the University of Bristol maintains a Molecule of the Month site that features user-contributed
articles, many of which involve Jmol applets as part of the
illustrations.

The issue in inorganic
chemistry for which Jmol has provided a general solution is the description
of symmetry. An example can be seen in a recent contribution at the Journal
of Chemical Education’s WebWare
site, a component of the JCE
Digital Library, which is a Collection within the National Science
Digital Library (NSDL). We
expect to see additional applications of Jmol within this area in the future
as Jmol develops and the newer features involving symmetry planes, rotational
axes, internal axis rotation, and internal coordinate referencing become more
widely known.

Table 2. Representative Uses of Jmol in General
and Inorganic Chemistry

http://www.webelements.com/
“WebElements aims to be a high quality source of chemistry information on
the WWW relating to the periodic table. Coverage is such that professional
scientists and students at school interested in chemistry and other
sciences will all find something useful.”

Access to the Jmol
structures is via the “elemental properties – Crystal structure” link on each element page.

3Dchem.com

http://www.3dchem.com
“Showing the world of chemistry and nano science in beautiful interactive
imagery. This web site highlights areas of the chemical world and
illustrates the structures behind the words. It also provides background
information about the science of the chemicals.”

When the user clicks on
any image of a molecule, a Jmol applet appears in a pop-up window. Controls
are provided.

http://www.edinformatics.com/interactive_molecules
“Explain it with Molecules -- Interactive Molecules-- is about "real
interactivity"! All you need is to be java enabled. The Jmol Applet
used with these molecular structures will allow you to view molecular
structures in 3-D. Images can be viewed as wire-frame, ball and stick or
CPK. As with the Chime plug-in, it is also possible to measure distances
and angles.”

CoolMolecules

http://www.stolaf.edu/depts/chemistry/mo/struc“All of the 962 structures in the full
database are actual, experimentally-determined structures. They are
displayed TO SCALE (100 pm = 1 cm on my screen). You can rotate them around
to see them from different angles, and you can double click on them to
check bond lengths and angles right on the model itself.”

Structures are delivered
to the browser as JavaScript arrays and then sent to the applet using
Jmol’s applet.loadInline() function.

VSEPR tutorial

http://www.uwosh.edu/faculty_staff/gutow/
VSEPR_TUTORIAL/VSEPR.html “This set of web pages is intended as a
tutorial on estimating the shape of a molecule once you have determined the
molecule's Lewis Structure.The
model used is often called the VSEPR (Valence Shell Electron Pair Repulsion)
model, and descriptions of it may be found in almost all introductory
chemistry texts.”

Introduction to VSEPR

http://winter.group.shef.ac.uk/vsepr“By arrangement with the publisher
(Oxford University Press), this introduction to VSEPR is a hypertext
version of Chapter 4 in my book on Chemical Bonding, one of the Oxford
Chemistry Primers.”

This site, like the previous
one, uses Jmol to depict atomic orbitals as probability.

Orbital

http://www.stolaf.edu/people/hansonr/orbital/
“ORBITAL.EXE is a Visual Basic 3.0 program that runs under Microsoft
Windows 9x. It allows students and presenters to produce probability-based
three-dimensional representations of the atomic orbitals of the hydrogen
atom. The orbitals are produced using a Monte Carlo technique and saved as XYZ files. These files are
suitable for uploading to web sites and are displayed automatically using
the default browser using the Jmol molecular viewer applet.”

http://www.chm.bris.ac.uk/motm/motm.htm
“Each month a new molecule will be added to the list on this page. The
links will take you to a page at one of the Web sites at a University
Chemistry Department or commercial site in the UK, the US, or anywhere in
the world, where useful (and hopefully entertaining!), information can be
found about a particularly interesting molecule.”

Molecules can be
displayed using a number of formats; the Java “JM” option selects Jmol as
the display applet.

“An Animated Interactive
Overview of Molecular Symmetry is a series of web pages designed to help
instructors teach molecular symmetry. These pages combine interactive
images and instructional text that allow students to examine and explore
the operations and elements that give rise to molecular symmetry.”

Jmol for Organic
Chemistry

We cannot hope to present
in this paper more than a small glimpse of the extensive use of Jmol that has
appeared in the area of organic chemistry. A recent Google search of “jmol
organic” returned “about 18,400” hits. In Table 3 we give only a small
sampling the many excellent sites on the Web, just as a way of illustrating
some of the variety of uses of Jmol. Topics cover a wide range, primarily
because so much of organic chemistry relies upon a visual understanding of
molecular structure and reactivity.

http://www.cem.msu.edu/~reusch/vtxtindex.htm“An interactive textbook covering the usual
topics treated in a college sophomore-level course. Links are offered to
advanced discussions of selected topics.” This understated description
accompanies the most extensive online discussion of organic chemistry ever
produced. It is, in fact, a complete, online textbook involving hundreds of
utilizations of Jmol.

http://cheminf.cmbi.ru.nl/wetche/organic/
“The WeTChe.NL tutorials are an initiative of the Faculty of Science, University of Nijmegen. The goal is to develop web based supplementary material for courses
in Chemistry, at all levels. The largest part of 'molecules in four
dimensions' is (at least at this moment) devoted to organic chemistry.”

Spectral Zoo

http://web.centre.edu/muzyka/organic/organic.htm
“This site includes Jmol-enabled tutorials to allow students to better understand
difficult organic chemistry concepts such as conformations, sterics, and
stereochemistry. There are also Jmol-enabled animations for substitution and
elimination reactions. The Spectral Zoo is a set of combined spectra which
serve as practice problems.”

Jmol/JSpecView

http://wwwchem.uwimona.edu.jm/spectra/JSpecView/
msanim/dodecaneJ/dodecane.html“JSpecView is a viewer for spectral
data in the JCAMP-DX format. Examples of
the combination of spectra and molecular graphics to show the interpretation
of simple IR, MS or NMR using JspecView and Jmol
are available.” This page uses several innovative aspects of Jmol, including
“designer” planes and the use of “show file” to transmit the contents of the
model file to JavaScript for further processing – in this case, determining
the masses of the fragments selected by the user.

http://www.rcsb.org/pdb “The
RCSB PDB provides a variety of tools and resources for studying the
structures of biological macromolecules and their relationships to sequence,
function, and disease. The RCSB is a member of the wwPDB, whose mission is to
ensure that the PDB archive remains an international resource with uniform
data. This site offers tools for browsing, searching, and reporting that
utilize the data resulting from ongoing efforts to create a more consistent
and comprehensive archive.” Jmol is one of the five viewers recommended by RCSB.

http://molvis.sdsc.edu/fgij
“FirstGlance in Jmol is a simple, free tool for macromolecular visualization.
The initial display is Cartoon plus Ligands+. Click on the links and buttons
above to see different aspects of the molecular structure.” Buttons show
informative views of any macromolecule available on-line. Help, including
color keys, appears automatically and is always in view. Hyperlinks show a molecule
in one click. It is designed to be useful both to novices and to specialists.

http://www.imb-jena.de/IMAGE.html
“The Jena Library of Biological Macromolecules (JenaLib) is aimed at a better
dissemination of information on three-dimensional biopolymer structures with
an emphasis on visualization and analysis. It provides access to all
structure entries deposited at the Protein Data Bank (PDB) or at the Nucleic
Acid Database (NDB). In addition, basic information on the architecture of
biopolymer structures is available.”

Jmol has found use in displaying
the structure of minerals. Sites utilizing Jmol are listed in Table 6. The
recently added connection and polyhedra capabilities of Jmol are expected to
expand this use considerably.

Table 6. Representative Uses of Jmol in Mineralogy and
Crystallography

http://webmineral.com/jmol/index.shtml
“This mineral database contains 4,442 individual mineral species descriptions
with links and a comprehensive image library.” Mineral Structure Index:
“Click on mineral name in the Index of Mineral Structures for a large
interactive display (Jmol Applet) of the chemical structure.”

The Virtual Museum of
Minerals and Molecules

http://virtual-museum.soils.wisc.edu
“The Virtual Museum of Minerals and Molecules™ is a web-based focal point and
resource for 3-D visualizations of molecules and minerals designed for
instructional use.”

This website is organized
along the lines of a typical museum with “wings” and “galleries” all devoted
to the structure of minerals.

With this website you can enter
crystal data from CIF files or manually based on symmetry or choose from a
list of crystal structures already on the server. After specifying the number
of unit cells, the structure is displayed using Jmol.

The recent addition of
“collapsed polyhedra” to Jmol (prototype version) has allowed the use of Jmol
to produce realistic-looking virtual equivalents of the precision scale
models created from paper.

Jmol in Textbooks

An exciting development has
been the utilization of Jmol by several publishers for mostly
biochemistry-related textbooks as the viewer of choice for their web site
ancillary material. Those we know of are listed in Table 5.

New to this edition: “Upgraded and re-designed web-based
media program to accompany and complement the text includes Interactive
Exercises, Guided Explorations, Animated Figures, as well as Kinemages. Media
resources have been upgraded to take advantage of the most recent,
web-friendly 3D visualization tools, eliminating the need for the Chime
plug-in, which has proven to be problematic.”

“The Second Edition has
been thoroughly revised and updated to incorporate the latest scientific
findings on popular topics such as disease-causing organisms and genetic
defects. Case study chapters have been placed throughout the book to tie
real-life scenarios into the concepts that follow. Two of the book’s key
pedagogical features, Discovery Questions and Math Minutes, have also been
updated and expanded. The interactive companion website has been reprogrammed
with JMOL, the latest 3-D software used to view DNA structures.”

Brooks-Cole General,
Organic, and Biochemistry Chemistry Textbooks

New to this edition: “Organic and Biochemistry OWL
content takes advantage of the latest technological advances in online computer
modeling using Jmol and Marvin Sketch. MarvinSketch, a Java applet for
viewing and drawing chemical structures, enables OWL to grade chemical
structures that the students draw and is used extensively in the content for
the Organic and Biochemistry chapters. Jmol, an interactive molecule viewer,
enables students to rotate molecules, to change the display mode (ball and
stick, space fill, etc.), and to measure bond distances and angles.”

Lehninger:

Principles of
Biochemistry

Future edition will incorporate
Jmol.

Stryer:

Biochemistry 6/e

Future edition will
incorporate Jmol.

Jmol in the Hands of
Instructors and Students

Examples of individual
instructors involving students in the use of Jmol are starting to appear on
the Web. For example, the online homework system, webassign, has recently
added a Jmol template. Jmol has also been integrated into the OWL system.Students at the University of Arizona in an honors introductory biochemistry course were asked to explore
the structure of brazzein for one of their homework assignments during the
Fall of 2005.[5]

Conclusions -- Future
Directions for Jmol

Jmol development relies solely
on the volunteer contributions of scientists, educators, and programmers.
Nonetheless, it is expected to be rapid during 2006. Areas currently under
active development are listed below. Links open experimental pages that
illustrate implementation of these goals within the very latest prototype
“trunk” of the development tree (trunk). We
welcome your comments, and we encourage you to get involved by joining the jmol users
list if you are interested in contributing to the discussion or the Jmol developers list
if you are interested in contributing at the developer level.

·Further
development of the application programming interface (API), which allows Jmol
to “talk” to other applications and applets.
[see AJAX]

Clearly, Jmol has come a
long way during the past few years and is rapidly becoming one of the most
popular Java applets in chemistry. Its strength is in its speed of rendering,
its flexibility in file reading, its broad applicability in both
small-molecule and macromolecule applications, and its ease of use.
Applications range from general chemistry to computational chemistry, from
inorganic chemistry to molecular biology to mineralogy and crystallography.
The applet is fast becoming far more than simply a tool for putting a
“gee-wiz” three-dimensional model of a molecule on the web. New capabilities
allow it to be an investigative tool as well, allowing the web
designer/user to gain access to information such as atomic charges, dipoles,
vibrational frequencies, space group symmetries, and molecular orbitals
contained in data-rich formats such as CIF, CDX, CML, and SMOL. Most
importantly, as an open-source project, the Jmol discussion lists have become
valuable forums for the discussion of important molecular visualization and
data analysis ideas among an energetic and dedicated group of scientists and
educators from all over the world.